Single HiC QC report
Processing
Run time
Started @ 2023-05-22 12:14:05
Finished @ 2023-05-22 12:14:29
Duration: 0 days, 00h 00min 24s
Processing directory
/__w/HiCool/HiCool/docs/reference
Reads location
R1:
/github/home/.cache/R/ExperimentHub/1fe971273e9d_7833
R2:
/github/home/.cache/R/ExperimentHub/1fe923fbe457_7834
Genome reference
/tmp/RtmpLG33tZ/R64-1-1
Command
x <- HiCool::HiCool(
r1 = "/github/home/.cache/R/ExperimentHub/1fe971273e9d_7833",
r2 = "/github/home/.cache/R/ExperimentHub/1fe923fbe457_7834",
genome = "/tmp/RtmpLG33tZ/R64-1-1",
resolutions = NA,
restriction = "DpnII,HinfI",
iterative = TRUE,
balancing_args = " --min-nnz 10 --mad-max 5 ",
threads = 1,
output = "./HiCool/",
exclude_chr = "Mito|chrM|MT",
keep_bam = FALSE,
scratch = "/tmp/RtmpLG33tZ"
)
Generated HiCExperiment object
x## CoolFile object
## .mcool file: /__w/HiCool/HiCool/docs/reference/HiCool/matrices/1fe971273e9d_7833^mapped-R64-1-1^DF8U6P.mcool
## resolution: 1000
## pairs file: /__w/HiCool/HiCool/docs/reference/HiCool/pairs/1fe971273e9d_7833^mapped-R64-1-1^DF8U6P.pairs
## metadata(3): log stats args
import(x)## `HiCExperiment` object with 60,836 contacts over 12,079 regions
## -------
## fileName: "/__w/HiCool/HiCool/docs/reference/HiCool/matrices/1fe971273e9d_7833^mapped-R64-1-1^DF8U6P.mcool"
## focus: "whole genome"
## resolutions(5): 1000 2000 4000 8000 16000
## active resolution: 1000
## interactions: 56522
## scores(2): count balanced
## topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0)
## pairsFile: /__w/HiCool/HiCool/docs/reference/HiCool/pairs/1fe971273e9d_7833^mapped-R64-1-1^DF8U6P.pairs
## metadata(3): log stats args
Mapping results
| Number of paired-end fragments | 100,000 |
| Total number of pairs after mapping | 73,993 |
| Number of valid pairs | 61,678 (83.36% of all pairs) |
| Number of unique valid pairs | 60,959 (82.38% of all pairs) |
| Number of pairs from uncut fragments (+-) | 10,027 (13.55% of all pairs) |
| Number of pairs from self-religated fragments (-+) | 2,205 (2.98% of all pairs) |
| Number of dumped pairs (– or ++) | 83 (0.11% of all pairs) |
Minimum # of restriction sites to retain `+-` pairs: 7
Minimum # of restriction sites to retain `-+` pairs: 7
Log file content
## HiCool working directory ::: /__w/HiCool/HiCool/docs/reference
## HiCool argument ::: r1: /github/home/.cache/R/ExperimentHub/1fe971273e9d_7833
## HiCool argument ::: r2: /github/home/.cache/R/ExperimentHub/1fe923fbe457_7834
## HiCool argument ::: genome: /tmp/RtmpLG33tZ/R64-1-1
## HiCool argument ::: resolutions:
## HiCool argument ::: restriction: DpnII,HinfI
## HiCool argument ::: iterative: TRUE
## HiCool argument ::: balancing_args: --min-nnz 10 --mad-max 5
## HiCool argument ::: threads: 1
## HiCool argument ::: output: ./HiCool/
## HiCool argument ::: exclude_chr: Mito|chrM|MT
## HiCool argument ::: keep_bam: FALSE
## HiCool argument ::: scratch: /tmp/RtmpLG33tZ
## ----------------
## ## hicstuff: v3.1.5 log file
## ## date: 2023-05-22 12:14:05
## ## enzyme: DpnII,HinfI
## ## input1: /github/home/.cache/R/ExperimentHub/1fe971273e9d_7833
## ## input2: /github/home/.cache/R/ExperimentHub/1fe923fbe457_7834
## ## ref: /tmp/RtmpLG33tZ/R64-1-1
## ---
## 2023-05-22,12:14:08 :: INFO :: 100000 reads to parse
## 2023-05-22,12:14:08 :: INFO :: Truncating unaligned reads to 20bp and mapping.
## 2023-05-22,12:14:11 :: INFO :: 19256 reads left to map.
## 2023-05-22,12:14:11 :: INFO :: Trying to map unaligned reads at full length (35bp).
## 2023-05-22,12:14:12 :: INFO :: 18387 reads left to map.
## 2023-05-22,12:14:12 :: INFO :: 81613 reads aligned / 100000 total reads.
## 2023-05-22,12:14:13 :: INFO :: 100000 reads to parse
## 2023-05-22,12:14:13 :: INFO :: Truncating unaligned reads to 20bp and mapping.
## 2023-05-22,12:14:16 :: INFO :: 20617 reads left to map.
## 2023-05-22,12:14:16 :: INFO :: Trying to map unaligned reads at full length (35bp).
## 2023-05-22,12:14:16 :: INFO :: 19373 reads left to map.
## 2023-05-22,12:14:17 :: INFO :: 80627 reads aligned / 100000 total reads.
## 2023-05-22,12:14:21 :: INFO :: 81% reads (single ends) mapped with Q >= 10.0 (162240/200000)
## 2023-05-22,12:14:24 :: INFO :: Filtering with thresholds: uncuts=7 loops=7
## 2023-05-22,12:14:25 :: INFO :: Proportion of inter contacts: 22.03% (intra: 48089, inter: 13589)
## 2023-05-22,12:14:25 :: INFO :: 12315 pairs discarded: Loops: 2205, Uncuts: 10027, Weirds: 83
## 2023-05-22,12:14:25 :: INFO :: 61678 pairs kept (83.36%)
## 2023-05-22,12:14:27 :: INFO :: 1% PCR duplicates have been filtered out (719 / 61678 pairs)
## 2023-05-22,12:14:29 :: INFO :: Contact map generated after 0h 0m 23s
Session information
System
## OS: Ubuntu 22.04.2 LTS
## system: x86_64, linux-gnu
## UI: X11
## R: 4.3.0(/usr/local/lib/R)
## Python: 3.7.12(/github/home/.cache/R/basilisk/1.13.0/HiCool/1.1.0/env/bin/python)
## Bioconductor: 3.18
## basilisk: 1.13.0
## HiCExperiment: 1.1.0
## HiCool: 1.1.0
System packages
## samtools: 1.16.1
## bowtie2: 2.5.0
R packages
## [3m[90mpackage [39m[23m [3m[90m*[39m[23m [3m[90mversion [39m[23m [3m[90mdate (UTC)[39m[23m [3m[90mlib[39m[23m [3m[90msource[39m[23m
## AnnotationDbi 1.63.1 [90m2023-05-02[39m [90m[1][39m [90mBioconductor[39m
## AnnotationHub * 3.9.1 [90m2023-05-01[39m [90m[1][39m [90mBioconductor[39m
## basilisk 1.13.0 [90m2023-05-19[39m [90m[1][39m [90mBioconductor[39m
## basilisk.utils 1.13.1 [90m2023-05-19[39m [90m[1][39m [90mBioconductor[39m
## Biobase 2.61.0 [90m2023-04-25[39m [90m[1][39m [90mBioconductor[39m
## BiocFileCache * 2.9.0 [90m2023-04-25[39m [90m[1][39m [90mBioconductor[39m
## BiocGenerics * 0.47.0 [90m2023-04-25[39m [90m[1][39m [90mBioconductor[39m
## BiocIO 1.11.0 [90m2023-04-25[39m [90m[1][39m [90mBioconductor[39m
## BiocManager 1.30.20 [90m2023-02-24[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## BiocParallel 1.35.1 [90m2023-05-05[39m [90m[1][39m [90mBioconductor[39m
## BiocVersion 3.18.0 [90m2023-04-25[39m [90m[2][39m [90mBioconductor[39m
## Biostrings 2.69.1 [90m2023-05-16[39m [90m[1][39m [90mBioconductor[39m
## bit 4.0.5 [90m2022-11-15[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## bit64 4.0.5 [90m2020-08-30[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## bitops 1.0-7 [90m2021-04-24[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## blob 1.2.4 [90m2023-03-17[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## bookdown 0.34 [90m2023-05-09[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## bslib 0.4.2 [90m2022-12-16[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## cachem 1.0.8 [90m2023-05-01[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## cli 3.6.1 [90m2023-03-23[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## codetools 0.2-19 [90m2023-02-01[39m [90m[3][39m [90mCRAN (R 4.3.0)[39m
## colorspace 2.1-0 [90m2023-01-23[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## crayon 1.5.2 [90m2022-09-29[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## crosstalk 1.2.0 [90m2021-11-04[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## curl 5.0.0 [90m2023-01-12[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## data.table 1.14.8 [90m2023-02-17[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## DBI 1.1.3 [90m2022-06-18[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## dbplyr * 2.3.2 [90m2023-03-21[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## DelayedArray 0.27.3 [90m2023-05-17[39m [90m[1][39m [90mBioconductor[39m
## desc 1.4.2 [90m2022-09-08[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## digest 0.6.31 [90m2022-12-11[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## dir.expiry 1.9.0 [90m2023-04-25[39m [90m[1][39m [90mBioconductor[39m
## downlit 0.4.2 [90m2022-07-05[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## dplyr 1.1.2 [90m2023-04-20[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## ellipsis 0.3.2 [90m2021-04-29[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## evaluate 0.21 [90m2023-05-05[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## ExperimentHub * 2.7.1 [90m2023-04-23[39m [90m[1][39m [90mBioconductor[39m
## fansi 1.0.4 [90m2023-01-22[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## fastmap 1.1.1 [90m2023-02-24[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## filelock 1.0.2 [90m2018-10-05[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## fs 1.6.2 [90m2023-04-25[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## generics 0.1.3 [90m2022-07-05[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## GenomeInfoDb 1.37.1 [90m2023-05-04[39m [90m[1][39m [90mBioconductor[39m
## GenomeInfoDbData 1.2.10 [90m2023-05-11[39m [90m[1][39m [90mBioconductor[39m
## GenomicRanges 1.53.1 [90m2023-05-04[39m [90m[1][39m [90mBioconductor[39m
## ggplot2 3.4.2 [90m2023-04-03[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## glue 1.6.2 [90m2022-02-24[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## gtable 0.3.3 [90m2023-03-21[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## here 1.0.1 [90m2020-12-13[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## HiCExperiment * 1.1.0 [90m2023-04-25[39m [90m[1][39m [90mBioconductor[39m
## HiContactsData * 1.3.0 [90m2023-04-27[39m [90m[1][39m [90mBioconductor[39m
## HiCool * 1.1.0 [90m2023-05-22[39m [90m[1][39m [90mBioconductor[39m
## htmltools 0.5.5 [90m2023-03-23[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## htmlwidgets 1.6.2 [90m2023-03-17[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## httpuv 1.6.11 [90m2023-05-11[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## httr 1.4.6 [90m2023-05-08[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## InteractionSet 1.29.0 [90m2023-04-25[39m [90m[1][39m [90mBioconductor[39m
## interactiveDisplayBase 1.39.0 [90m2023-04-25[39m [90m[1][39m [90mBioconductor[39m
## IRanges 2.35.1 [90m2023-05-03[39m [90m[1][39m [90mBioconductor[39m
## jquerylib 0.1.4 [90m2021-04-26[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## jsonlite 1.8.4 [90m2022-12-06[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## KEGGREST 1.41.0 [90m2023-04-25[39m [90m[1][39m [90mBioconductor[39m
## knitr 1.42 [90m2023-01-25[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## later 1.3.1 [90m2023-05-02[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## lattice 0.21-8 [90m2023-04-05[39m [90m[3][39m [90mCRAN (R 4.3.0)[39m
## lazyeval 0.2.2 [90m2019-03-15[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## lifecycle 1.0.3 [90m2022-10-07[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## magrittr 2.0.3 [90m2022-03-30[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## Matrix 1.5-4.1 [90m2023-05-18[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## MatrixGenerics 1.13.0 [90m2023-04-25[39m [90m[1][39m [90mBioconductor[39m
## matrixStats 0.63.0 [90m2022-11-18[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## memoise 2.0.1 [90m2021-11-26[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## mime 0.12 [90m2021-09-28[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## munsell 0.5.0 [90m2018-06-12[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## pillar 1.9.0 [90m2023-03-22[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## pkgconfig 2.0.3 [90m2019-09-22[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## pkgdown 2.0.7 [90m2022-12-14[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## plotly 4.10.1 [90m2022-11-07[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## png 0.1-8 [90m2022-11-29[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## promises 1.2.0.1 [90m2021-02-11[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## purrr 1.0.1 [90m2023-01-10[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## R6 2.5.1 [90m2021-08-19[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## ragg 1.2.5 [90m2023-01-12[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## rappdirs 0.3.3 [90m2021-01-31[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## Rcpp 1.0.10 [90m2023-01-22[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## RCurl 1.98-1.12 [90m2023-03-27[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## reticulate 1.28 [90m2023-01-27[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## rhdf5 2.45.0 [90m2023-04-25[39m [90m[1][39m [90mBioconductor[39m
## rhdf5filters 1.13.2 [90m2023-04-30[39m [90m[1][39m [90mBioconductor[39m
## Rhdf5lib 1.23.0 [90m2023-04-25[39m [90m[1][39m [90mBioconductor[39m
## rlang 1.1.1 [90m2023-04-28[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## rmarkdown 2.21 [90m2023-03-26[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## rmdformats 1.0.4 [90m2022-05-17[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## rprojroot 2.0.3 [90m2022-04-02[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## RSQLite 2.3.1 [90m2023-04-03[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## rstudioapi 0.14 [90m2022-08-22[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## S4Arrays 1.1.4 [90m2023-05-14[39m [90m[1][39m [90mBioconductor[39m
## S4Vectors 0.39.1 [90m2023-05-03[39m [90m[1][39m [90mBioconductor[39m
## sass 0.4.6 [90m2023-05-03[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## scales 1.2.1 [90m2022-08-20[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## sessioninfo 1.2.2 [90m2021-12-06[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## shiny 1.7.4 [90m2022-12-15[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## SparseArray 1.1.5 [90m2023-05-17[39m [90m[1][39m [90mBioconductor[39m
## strawr 0.0.91 [90m2023-03-29[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## stringi 1.7.12 [90m2023-01-11[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## stringr 1.5.0 [90m2022-12-02[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## SummarizedExperiment 1.31.1 [90m2023-05-01[39m [90m[1][39m [90mBioconductor[39m
## systemfonts 1.0.4 [90m2022-02-11[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## textshaping 0.3.6 [90m2021-10-13[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## tibble 3.2.1 [90m2023-03-20[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## tidyr 1.3.0 [90m2023-01-24[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## tidyselect 1.2.0 [90m2022-10-10[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## tzdb 0.4.0 [90m2023-05-12[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## utf8 1.2.3 [90m2023-01-31[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## vctrs 0.6.2 [90m2023-04-19[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## viridisLite 0.4.2 [90m2023-05-02[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## vroom 1.6.3 [90m2023-04-28[39m [90m[1][39m [90mCRAN (R 4.3.0)[39m
## whisker 0.4.1 [90m2022-12-05[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## withr 2.5.0 [90m2022-03-03[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## xfun 0.39 [90m2023-04-20[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## xml2 1.3.4 [90m2023-04-27[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## xtable 1.8-4 [90m2019-04-21[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## XVector 0.41.1 [90m2023-05-03[39m [90m[1][39m [90mBioconductor[39m
## yaml 2.3.7 [90m2023-01-23[39m [90m[2][39m [90mCRAN (R 4.3.0)[39m
## zlibbioc 1.47.0 [90m2023-04-25[39m [90m[1][39m [90mBioconductor[39m
##
## [90m [1] /__w/_temp/Library[39m
## [90m [2] /usr/local/lib/R/site-library[39m
## [90m [3] /usr/local/lib/R/library[39m
Python environment
## python: /github/home/.cache/R/basilisk/1.13.0/HiCool/1.1.0/env/bin/python
## libpython: /github/home/.cache/R/basilisk/1.13.0/HiCool/1.1.0/env/lib/libpython3.7m.so
## pythonhome: /github/home/.cache/R/basilisk/1.13.0/HiCool/1.1.0/env:/github/home/.cache/R/basilisk/1.13.0/HiCool/1.1.0/env
## version: 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:53) [GCC 9.4.0]
## numpy: /github/home/.cache/R/basilisk/1.13.0/HiCool/1.1.0/env/lib/python3.7/site-packages/numpy
## numpy_version: 1.21.6
##
## NOTE: Python version was forced by use_python function
Python packages
## full package
## 1 asciitree==0.3.3 asciitree
## 2 attrs==23.1.0 attrs
## 3 biopython==1.79 biopython
## 4 bokeh==2.4.3 bokeh
## 5 Bottleneck==1.3.5 Bottleneck
## 6 brotlipy==0.7.0 brotlipy
## 7 cached-property==1.5.2 cached-property
## 8 certifi==2023.5.7 certifi
## 9 cffi==1.15.1 cffi
## 10 charset-normalizer==3.1.0 charset-normalizer
## 11 chromosight==1.6.3 chromosight
## 12 click==8.1.3 click
## 13 cloudpickle==2.2.1 cloudpickle
## 14 cooler==0.9.1 cooler
## 15 cryptography==38.0.2 cryptography
## 16 cycler==0.11.0 cycler
## 17 cytoolz==0.12.0 cytoolz
## 18 dask==2021.10.0 dask
## 19 dill==0.3.6 dill
## 20 distributed==2021.10.0 distributed
## 21 docopt==0.6.2 docopt
## 22 fonttools==4.38.0 fonttools
## 23 fsspec==2023.1.0 fsspec
## 24 h5py==3.7.0 h5py
## 25 HeapDict==1.0.1 HeapDict
## 26 hicstuff==3.1.5 hicstuff
## 27 idna==3.4 idna
## 28 importlib-metadata==4.11.4 importlib-metadata
## 29 importlib-resources==5.12.0 importlib-resources
## 30 Jinja2==3.1.2 Jinja2
## 31 joblib==1.2.0 joblib
## 32 jsonschema==4.17.3 jsonschema
## 33 kiwisolver==1.4.4 kiwisolver
## 34 locket==1.0.0 locket
## 35 MarkupSafe==2.1.1 MarkupSafe
## 36 matplotlib==3.5.3 matplotlib
## 37 msgpack==1.0.4 msgpack
## 38 multiprocess==0.70.14 multiprocess
## 39 munkres==1.1.4 munkres
## 40 numexpr==2.8.3 numexpr
## 41 numpy==1.21.6 numpy
## 42 packaging==23.1 packaging
## 43 pandas==1.3.5 pandas
## 44 partd==1.4.0 partd
## 45 Pillow==9.2.0 Pillow
## 46 pip==23.1.2 pip
## 47 pkgutil_resolve_name==1.3.10 pkgutil_resolve_name
## 48 psutil==5.9.3 psutil
## 49 pycparser==2.21 pycparser
## 50 pyfaidx==0.7.2.1 pyfaidx
## 51 pyfastx==1.1.0 pyfastx
## 52 pyOpenSSL==23.1.1 pyOpenSSL
## 53 pypairix==0.3.7 pypairix
## 54 pyparsing==3.0.9 pyparsing
## 55 pyrsistent==0.18.1 pyrsistent
## 56 pysam==0.21.0 pysam
## 57 PySocks==1.7.1 PySocks
## 58 python-dateutil==2.8.2 python-dateutil
## 59 pytz==2023.3 pytz
## 60 PyVCF3==1.0.3 PyVCF3
## 61 PyYAML==6.0 PyYAML
## 62 requests==2.29.0 requests
## 63 scikit-learn==1.0.2 scikit-learn
## 64 scipy==1.7.3 scipy
## 65 setuptools==67.7.2 setuptools
## 66 simplejson==3.17.6 simplejson
## 67 six==1.16.0 six
## 68 sortedcontainers==2.4.0 sortedcontainers
## 69 tblib==1.7.0 tblib
## 70 threadpoolctl==3.1.0 threadpoolctl
## 71 toolz==0.12.0 toolz
## 72 tornado==6.2 tornado
## 73 typing_extensions==4.5.0 typing_extensions
## 74 unicodedata2==14.0.0 unicodedata2
## 75 urllib3==1.26.15 urllib3
## 76 wheel==0.40.0 wheel
## 77 zict==2.2.0 zict
## 78 zipp==3.15.0 zipp